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Theoretical and Computational Chemistry

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Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Xujian Wang, Xiongwu Wu, Bernard Brooks, Junmei Wang

Version 2 posted 07 March 2025

730

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Physical Chemistry

Working Paper

Comprehensive analysis of nitrile probe IR shifts and intensities in proteins: experiment and critical evaluation of simulations

Jacob M. Kirsh, Jared Bryce Weaver, Steven G. Boxer, Jacek Kozuch

Version 2 posted 02 January 2024

475

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1

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Theoretical and Computational Chemistry

Working Paper

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Aliza Rubenstein, Kristin Blacklock, Hai Nguyen, David Case, Sagar Khare

Version 2 posted 04 April 2018

1,666

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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,850

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2

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Biological and Medicinal Chemistry

Working Paper

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Thomas Fellowes, JONATHAN WHITE

Version 2 posted 05 May 2021

717

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Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

607

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1

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Theoretical and Computational Chemistry

Working Paper

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Vinicius Cruzeiro, Gustavo Troiano Feliciano, Adrian Roitberg

Version 1 posted 03 February 2020

493

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Theoretical and Computational Chemistry

Working Paper

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Junjie Zou, Chuan Tian, Carlos Simmerling

Version 1 posted 24 June 2019

1,131

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Theoretical and Computational Chemistry

Working Paper

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

3,380

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1

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Biological and Medicinal Chemistry

Working Paper

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg

Version 1 posted 18 June 2019

814

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18 results in Amber in Keywords: Amber

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Comprehensive analysis of nitrile probe IR shifts and intensities in proteins: experiment and critical evaluation of simulations

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Validation of AMBER/GAFF for Relative Free Energy Calculations

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

A Fast Implementation of the Nudged Elastic Band Method in AMBER

18 results in Keywords: Amber